Use dynamic package version and respect CODEQL_MCP_TMP_DIR env var

server/src/lib/cli-tool-registry.ts

@@ -8,7 +8,7 @@ import { executeCodeQLCommand, executeQLTCommand, CLIExecutionResult } from './c
 import { logger } from '../utils/logger';
 import { evaluateQueryResults, QueryEvaluationResult, extractQueryMetadata } from './query-results-evaluator';
 import { getOrCreateLogDirectory } from './log-directory-manager';
-import { packageRootDir, resolveToolQueryPackPath, workspaceRootDir } from '../utils/package-paths';
+import { getUserWorkspaceDir, packageRootDir, resolveToolQueryPackPath } from '../utils/package-paths';
 import { writeFileSync, rmSync, existsSync, mkdirSync } from 'fs';
 import { basename, dirname, isAbsolute, join, resolve } from 'path';
 import { createProjectTempDir } from '../utils/temp-dir';
@@ -215,19 +215,21 @@ export function registerCLITool(server: McpServer, definition: CLIToolDefinition
           case 'codeql_test_run':
           case 'codeql_resolve_tests':
             // Handle tests parameter as positional arguments for test tools.
-            // Resolve relative paths against workspaceRootDir since the MCP
-            // server's cwd may not be the repo root.
+            // Resolve relative paths against the user's effective workspace
+            // directory. In monorepo layouts this is the repo root; in npm-
+            // installed layouts it falls back to process.cwd().
             if (tests && Array.isArray(tests)) {
+              const userDir = getUserWorkspaceDir();
               positionalArgs = [...positionalArgs, ...(tests as string[]).map(
-                t => isAbsolute(t) ? t : resolve(workspaceRootDir, t)
+                t => isAbsolute(t) ? t : resolve(userDir, t)
               )];
             }
             break;
 
           case 'codeql_query_run': {
             // Resolve database path to absolute path if it's relative
             if (options.database && typeof options.database === 'string' && !isAbsolute(options.database)) {
-              options.database = resolve(workspaceRootDir, options.database);
+              options.database = resolve(getUserWorkspaceDir(), options.database);
               logger.info(`Resolved database path to: ${options.database}`);
             }
 
@@ -389,9 +391,9 @@ export function registerCLITool(server: McpServer, definition: CLIToolDefinition
           let cwd: string | undefined;
           if ((name === 'codeql_pack_install' || name === 'codeql_pack_ls') && (dir || packDir)) {
             const rawCwd = (dir || packDir) as string;
-            // Resolve relative paths against the workspace root, not process.cwd(),
-            // since the MCP server's cwd may differ (especially in VS Code).
-            cwd = isAbsolute(rawCwd) ? rawCwd : resolve(workspaceRootDir, rawCwd);
+            // Resolve relative paths against the user's effective workspace
+            // directory rather than a potentially read-only package root.
+            cwd = isAbsolute(rawCwd) ? rawCwd : resolve(getUserWorkspaceDir(), rawCwd);
           }
 
           // Add --additional-packs for commands that need to access local test packs.

server/src/lib/language-server.ts

@@ -9,6 +9,7 @@ import { setTimeout, clearTimeout } from 'timers';
 import { pathToFileURL } from 'url';
 import { delimiter, join } from 'path';
 import { logger } from '../utils/logger';
+import { getPackageVersion } from '../utils/package-paths';
 import { getProjectTmpDir } from '../utils/temp-dir';
 import { getResolvedCodeQLDir } from './cli-executor';
 
@@ -243,7 +244,7 @@ export class CodeQLLanguageServer extends EventEmitter {
       processId: process.pid,
       clientInfo: {
         name: 'codeql-development-mcp-server',
-        version: '2.23.9'
+        version: getPackageVersion()
       },
       capabilities: {
         textDocument: {

server/src/lib/session-data-manager.ts

@@ -8,7 +8,7 @@ import { JSONFileSync } from 'lowdb/node';
 import { mkdirSync, writeFileSync } from 'fs';
 import { join } from 'path';
 import { randomUUID } from 'crypto';
-import { getPackageRootDir } from '../utils/package-paths';
+import { getProjectTmpBase } from '../utils/temp-dir';
 import {
   QueryDevelopmentSession,
   QueryState,
@@ -403,6 +403,6 @@ function parseBoolEnv(envVar: string | undefined, defaultValue: boolean): boolea
 
 // Export singleton instance with environment variable support
 export const sessionDataManager = new SessionDataManager({
-  storageLocation: process.env.MONITORING_STORAGE_LOCATION || join(getPackageRootDir(), '.ql-mcp-tracking'),
+  storageLocation: process.env.MONITORING_STORAGE_LOCATION || join(getProjectTmpBase(), '.ql-mcp-tracking'),
   enableMonitoringTools: parseBoolEnv(process.env.ENABLE_MONITORING_TOOLS, false),
 });